Annotation

Module to handle label and annotation info from Allen Brain Atlas (v2).

Notes

• The files containting annotation information is assumed to be in the path stored in atlas_path, which defaults to the resource path ClearMap.Settings.resources_path.

• The annotation file is assumed to be ‘annotation_25_full.nrrd’ but can be set via default_annotation_file.

• The mapping between labels and brain area information is assumed to be in the ‘annotation.json’ file but the location can be set via default_label_file.

References

• Allen Brain Atlas

class Annotation(label_file=None, extra_label=None, annotation_file=None)

Bases: object

Class that holds information of the annotated regions.

add_data(name, data)

common_parent(label, key='id', value=None)

convert_label(label, key='order', value='graph_order', node=None, level=None, method='map')

find(label, key='id', value=None, node=None, level=None)

get_dictionary(key, value, node=None, level=None, ordered=False)

get_hierarchical_dictionary(node=None)

get_list(key=None, node=None, level=None)

get_map(key, value, node=None, level=None)

initialize(label_file=None, extra_label=None, annotation_file=None)

initialze_tree(root, parent=None, level=0)

label_to_color(label, key='order', level=None, alpha=True, as_int=False, int_type='uint8')

parents(label, key='id', value=None)

property max_level

property n_structures

class Label(data, children=None, parent=None, level=0)

Bases: object

Class holding information of an individual Atlas label.

color(*args, **kwargs)

info(with_children=True, ident=None)

write(with_children=True, ident=None)

property id

property level

property name

property order

color_map(alpha=True, as_int=False, int_type='uint8')

Generates a color map from color ids to rgb

Arguments

alphabool

If True return a color map with alpha values.

Returns

color_maparray

An array of rgb colors for each label.

convert_label(label, key='id', value='order', level=None, method=None)

Convert label using the atlas annotation data.

Arguments

lablearray

List of labels to convert.

keystr

The key corresponding to the label.

valuestr

The key to ocnvert the lable to.

levelnt or None

Convert at this level of the hierarchy. I fNone use full hierarchy.

method‘map’ or ‘dictionary’

Convert labels using a mapping array or a dictionary. Depending on the keys either can be faster for large data sets.

Returns

labelarray

List of converted labels.

convert_label_to_color(label, key='id', level=None, alpha=True, as_int=False, int_type='uint8')

Convert label using the atlas annotation colors.

Arguments

lablearray

List of labels to convert.

keystr

The key corresponding to the label.

levelnt or None

Convert at this level of the hierarchy. I fNone use full hierarchy.

alphabool

If True, return rgba values.

as_intbool

If True, return rgb valueas as int between 0 and 255.

int_typedtype

Type for the color array.

Returns

colorsarray

List of colors for each label.

count_label(label, weights=None, key='order', hierarchical=True)

Counts the label within the various structures, taking into account the sub-structures.

Arguments

labelarray

List of labels.

weightsarray

Optional list of weights for each label.

keystr

The key the lables are given in.

hierarchicalbool

If True, count all sub-labels.

Returns

binsarray

The counts for each label.

count_points(points, weights=None, annotation_file=None, invalid=0, hierarchical=True)

Counts the points within the various structures, taking into account the sub-structures.

Arguments

pointsarray

Array of nxdim points to annotate and count.

weightsarray or None

Optional intensity values to weight the count.

annotation_filestr

File name of the atlas annotation.

invalidint

Label for invalid points.

hierarchicalbool

If True, count all sub-labels.

Returns

binsarray

The counts for each label.

find(label, key='id', value=None, node=None, level=None)

format_annotation_filename(filename, orientation=None, slicing=None, postfix=None, directory=None)

Formats the annotation filename given oriantion and slicing.

get_dictionary(key, value, node=None, level=None, ordered=False)

get_list(key=None, node=None, level=None)

get_map(key, value, node=None, level=None)

initialize(label_file=None, extra_label=None, annotation_file=None)

label_points(points, annotation_file=None, invalid=0, key='order', level=None)

Label points according to the annotation in the labeled image file.

Arguments

pointsarray

Array of nxdim point coordinates to be labeled.

annotation_filestr

File name of the atals annotation.

invalidint

Label for invalid points.

keystr

The key of the label, by default the order of the labels.

Returns

labelarray

Label of the points corresponding to the given key.

prepare_annotation_files(slicing=None, orientation=None, directory=None, postfix=None, annotation_file=None, reference_file=None, distance_to_surface_file=None, overwrite=False, verbose=False)

Crop the annotation, reference and distance files to match the data.

Arguments

slicingtuple or None

The slice specification after reorienting.

orientationtuple, str or None.

The orientation specification. Strings can be ‘left’ or ‘right’, for the two hemispheres.

directorystr or None

The target directory. If None, use ClearMap resources folder.

postfixstr or None

Use this postfix for the cropped annotation file. If None and automatic label is choosen.

annotation_filestr or None

The annotation file to use.

reference_filestr or None

The reference file to use.

distance_to_surface_filestr or None

The distance file to use.

overwritebool

If True, overwrite exisitng files.

Returns

annotation_filestr

The cropped annotation file.

reference_filestr

The cropped reference file.

distance_to_surface_filestr

The distance cropped file.

set_annotation_file(annotation_file)

set_label_file(label_file, extra_label=None)

write_color_annotation(filename, annotation_file=None)

Creates a rgb image from the atlas color data.

Arguments

filenamestr

The name of the color palette file.

annotation_filestr

File name of the atals annotation.

Returns

filenamestr

The name of the file to which the color atlas was written.

write_color_palette(filename=None)

Creates a pal or lut file for imaris or imagej based on label colors of atlas.

Arguments

filenamestr

The name of the color palette file.

Returns

filenamestr

The name of the file to which the color palette was written.

annotation = Annotation(1319)[11]{/home/ckirst/Programs/ClearMap2/ClearMap/Resources/Atlas/ABA_annotation.json}

Information on the annotated regions

atlas_path = '/home/ckirst/Programs/ClearMap2/ClearMap/Resources/Atlas'

Default path to atlas infomration.

default_annotation_file = '/home/ckirst/Programs/ClearMap2/ClearMap/Resources/Atlas/ABA_25um_annotation.tif'

Default volumetric annotated image file.

Note

This file is by default the Allen brain annotated mouse atlas with 25um isotropic resolution.

default_distance_to_surface_file = '/home/ckirst/Programs/ClearMap2/ClearMap/Resources/Atlas/ABA_25um_distance_to_surface.tif'

Default volumetric annotated image file.

Note

This file is by default the Allen brain annotated mouse atlas with 25um isotropic resolution.

default_extra_label = [(182305696, 453, 'No label', 'NoL'), (182305712, 453, 'No label', 'NoL'), (312782560, 315, 'No label', 'NoL'), (312782592, 453, 'No label', 'NoL'), (312782656, 315, 'No label', 'NoL'), (526157184, 993, 'No label', 'NoL'), (526322272, 500, 'No label', 'NoL'), (527696992, 315, 'No label', 'NoL')]

Additional label not in the Allen Brain Atlas label but in the atlas image.

Note

The form is a list of tuples, each tuple has the form (atlas id, parent id, name, acronym).

default_label_file = '/home/ckirst/Programs/ClearMap2/ClearMap/Resources/Atlas/ABA_annotation.json'

Default list of labels and region names in the annotated image.

Note

This file is by default the labels for the Allen brain annotated mouse atlas with 25um isotropic resolution.

default_reference_file = '/home/ckirst/Programs/ClearMap2/ClearMap/Resources/Atlas/ABA_25um_reference.tif'

Default volumetric annotated image file.

Note

This file is by default the Allen brain annotated mouse atlas with 25um isotropic resolution.